On Thursday and Friday Haftar's self-styled Libyan National Army (LNA) launched air strikes on Zuwara airport in western Libya, targeting what it said was a hangar "which houses Turkish drones and their ammunition".
The Tripoli-based Government of National Accord -- recognised by the UN -- said a member of civil protection was wounded in Friday's attack.
UNSMIL said it dispatched a delegation to Zuwara to investigate the LNA allegations.
"After reviewing the airport's facilities and all the adjacent buildings, the assessment mission was able to confirm that neither military assets nor military infrastructure were observed at Zuwara Airport," a statement said.
It declared Zuwara airport "a civilian facility".
UNSMIL denounced the strike, which "caused serious damage to the airport's infrastructure, including to the runway".
"Attacks against civilians and civilian infrastructures constitute a grave violation of international humanitarian and human rights law," it said.
Haftar's forces have also allegedly repeatedly targeted Tripoli's sole functioning airport Mitiga.
The GNA said rocket fire there earlier this month killed a guard and wounded several security agents, prompting a temporary suspension of flights.
Haftar launched an offensive in April to seize Tripoli from the GNA.
The two sides have since been embroiled in a stalemate on the capital's southern outskirts.
Since April, the fighting has killed at least 1,093 people and wounded 5,752, while some 120,000 others have been displaced, according to the World Health Organization.